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Protein sequence threading: Averaging over structures
Author(s) -
Russell Anthony J.,
Torda Andrew E.
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10088
Subject(s) - threading (protein sequence) , sequence (biology) , protein structure prediction , structural alignment , loop modeling , sequence alignment , computer science , alignment free sequence analysis , multiple sequence alignment , protein structure , similarity (geometry) , protein sequencing , computational biology , set (abstract data type) , protein superfamily , protein secondary structure , algorithm , bioinformatics , peptide sequence , artificial intelligence , biology , genetics , gene , biochemistry , image (mathematics) , programming language
Multiple sequence alignments are a routine tool in protein fold recognition, but multiple structure alignments are computationally less cooperative. This work describes a method for protein sequence threading and sequence‐to‐structure alignments that uses multiple aligned structures, the aim being to improve models from protein threading calculations. Sequences are aligned into a field due to corresponding sites in homologous proteins. On the basis of a test set of more than 570 protein pairs, the procedure does improve alignment quality, although no more than averaging over sequences. For the force field tested, the benefit of structure averaging is smaller than that of adding sequence similarity terms or a contribution from secondary structure predictions. Although there is a significant improvement in the quality of sequence‐to‐structure alignments, this does not directly translate to an immediate improvement in fold recognition capability. Proteins 2002;47:496–505. © 2002 Wiley‐Liss, Inc.